Multiple sequence alignment - TraesCS4A01G053600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G053600 chr4A 100.000 2427 0 0 1 2427 45263345 45265771 0 4482
1 TraesCS4A01G053600 chr5A 93.763 2421 131 14 15 2427 232660981 232663389 0 3616
2 TraesCS4A01G053600 chr2A 92.957 2442 145 20 1 2427 490628574 490631003 0 3531
3 TraesCS4A01G053600 chr3A 92.737 2437 136 17 1 2427 727905092 727902687 0 3482
4 TraesCS4A01G053600 chr6A 92.115 2435 170 19 1 2427 401500581 401498161 0 3413
5 TraesCS4A01G053600 chr6A 91.133 2436 187 27 1 2427 178096006 178093591 0 3275
6 TraesCS4A01G053600 chr1A 90.842 2435 172 34 1 2427 252751399 252753790 0 3214
7 TraesCS4A01G053600 chr7A 90.617 2462 164 37 1 2427 206736612 206734183 0 3205
8 TraesCS4A01G053600 chr4D 88.821 2442 231 34 1 2427 179916663 179919077 0 2959
9 TraesCS4A01G053600 chr7D 88.775 2441 231 35 1 2427 122700579 122698168 0 2950
10 TraesCS4A01G053600 chr5D 88.310 2438 244 35 1 2427 464309997 464312404 0 2885


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G053600 chr4A 45263345 45265771 2426 False 4482 4482 100.000 1 2427 1 chr4A.!!$F1 2426
1 TraesCS4A01G053600 chr5A 232660981 232663389 2408 False 3616 3616 93.763 15 2427 1 chr5A.!!$F1 2412
2 TraesCS4A01G053600 chr2A 490628574 490631003 2429 False 3531 3531 92.957 1 2427 1 chr2A.!!$F1 2426
3 TraesCS4A01G053600 chr3A 727902687 727905092 2405 True 3482 3482 92.737 1 2427 1 chr3A.!!$R1 2426
4 TraesCS4A01G053600 chr6A 401498161 401500581 2420 True 3413 3413 92.115 1 2427 1 chr6A.!!$R2 2426
5 TraesCS4A01G053600 chr6A 178093591 178096006 2415 True 3275 3275 91.133 1 2427 1 chr6A.!!$R1 2426
6 TraesCS4A01G053600 chr1A 252751399 252753790 2391 False 3214 3214 90.842 1 2427 1 chr1A.!!$F1 2426
7 TraesCS4A01G053600 chr7A 206734183 206736612 2429 True 3205 3205 90.617 1 2427 1 chr7A.!!$R1 2426
8 TraesCS4A01G053600 chr4D 179916663 179919077 2414 False 2959 2959 88.821 1 2427 1 chr4D.!!$F1 2426
9 TraesCS4A01G053600 chr7D 122698168 122700579 2411 True 2950 2950 88.775 1 2427 1 chr7D.!!$R1 2426
10 TraesCS4A01G053600 chr5D 464309997 464312404 2407 False 2885 2885 88.310 1 2427 1 chr5D.!!$F1 2426

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
29 30 0.035343 GAAGTGCCACCCCTAGTTCC 60.035 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1491 0.035317 AGCTCAACGACCATTGCAGA 59.965 50.0 0.0 0.0 0.0 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.843851 CCATTAGAAGTGCCACCCCTA 59.156 52.381 0.00 0.00 0.00 3.53
29 30 0.035343 GAAGTGCCACCCCTAGTTCC 60.035 60.000 0.00 0.00 0.00 3.62
78 79 1.043816 ACCTGCGGATGACTATGAGG 58.956 55.000 0.00 0.00 0.00 3.86
106 108 2.309755 TCAAGGCCACAAGGATCAGAAT 59.690 45.455 5.01 0.00 36.89 2.40
169 171 2.211250 ACAGCAAGCACATGAAGGAT 57.789 45.000 0.00 0.00 0.00 3.24
224 226 7.038048 CCCTCATTTGCTTTCCTCTTTATTTC 58.962 38.462 0.00 0.00 0.00 2.17
266 269 8.803201 TCTATAGATGCTCTGTTTACGATTTG 57.197 34.615 0.00 0.00 0.00 2.32
336 343 5.363562 TTTCATACAGCTCATGTCTGGAT 57.636 39.130 17.46 13.39 42.70 3.41
389 396 1.336887 CGTTGACCTCGGTGATCTTGT 60.337 52.381 0.00 0.00 0.00 3.16
576 584 0.317799 TTGCTGCGCATGGTGATTTT 59.682 45.000 12.24 0.00 38.76 1.82
903 924 6.539826 TGTCATTCATGTACCTCTAATTGCAG 59.460 38.462 0.00 0.00 0.00 4.41
907 928 1.828595 TGTACCTCTAATTGCAGCCGA 59.171 47.619 0.00 0.00 0.00 5.54
1030 1060 0.595095 GTTCCAAGAGCTTGCACCAG 59.405 55.000 4.72 0.00 39.16 4.00
1034 1064 0.959372 CAAGAGCTTGCACCAGAGGG 60.959 60.000 0.00 0.00 35.34 4.30
1354 1389 7.420002 TGAAGTTGATGATTTTCTGTGTTCTG 58.580 34.615 0.00 0.00 0.00 3.02
1426 1463 4.211125 TGTTGGAATACCTTGCAAAGTGA 58.789 39.130 11.02 0.00 43.21 3.41
1454 1491 2.646175 CGGGTCCCTGTCGTCACAT 61.646 63.158 6.29 0.00 0.00 3.21
1540 1578 3.966215 CGGTCCAACGCACAAGAT 58.034 55.556 0.00 0.00 0.00 2.40
1554 1592 4.872691 CGCACAAGATTTCATAGAGGAAGT 59.127 41.667 0.00 0.00 0.00 3.01
1576 1614 5.047377 AGTTGTCAAGAAAGCCAACAAGAAA 60.047 36.000 0.00 0.00 39.63 2.52
1791 1830 2.363038 ACCTACTTACGTGTGACAGCAA 59.637 45.455 0.00 0.00 0.00 3.91
1882 1924 5.063944 GCGTCTATGATGTCTGAAAACATGT 59.936 40.000 0.00 0.00 39.93 3.21
1944 1988 3.055747 TCTTTTCCGTTTGGCTTTTTGGT 60.056 39.130 0.00 0.00 34.14 3.67
1945 1989 2.301577 TTCCGTTTGGCTTTTTGGTG 57.698 45.000 0.00 0.00 34.14 4.17
1976 2021 6.755206 TGCATTGCTAACTATATCGGTTAGT 58.245 36.000 20.19 1.18 44.47 2.24
1978 2023 8.027189 TGCATTGCTAACTATATCGGTTAGTAG 58.973 37.037 20.19 11.88 44.47 2.57
1979 2024 8.027771 GCATTGCTAACTATATCGGTTAGTAGT 58.972 37.037 20.19 14.23 44.47 2.73
2007 2052 0.388659 TACACAGCCGTAACCGTGTT 59.611 50.000 0.00 0.00 42.35 3.32
2158 2204 7.012327 GCATATTCAGTAGAACTAACATGGCAA 59.988 37.037 0.00 0.00 36.39 4.52
2213 2305 3.211865 ACATGCATGGCAGATTCAGTAG 58.788 45.455 29.41 0.42 43.65 2.57
2214 2306 3.118149 ACATGCATGGCAGATTCAGTAGA 60.118 43.478 29.41 0.00 43.65 2.59
2215 2307 3.632643 TGCATGGCAGATTCAGTAGAA 57.367 42.857 0.00 0.00 34.32 2.10
2216 2308 3.954200 TGCATGGCAGATTCAGTAGAAA 58.046 40.909 0.00 0.00 33.83 2.52
2217 2309 4.334552 TGCATGGCAGATTCAGTAGAAAA 58.665 39.130 0.00 0.00 33.83 2.29
2218 2310 4.397103 TGCATGGCAGATTCAGTAGAAAAG 59.603 41.667 0.00 0.00 33.83 2.27
2219 2311 4.201990 GCATGGCAGATTCAGTAGAAAAGG 60.202 45.833 0.00 0.00 37.29 3.11
2220 2312 4.640771 TGGCAGATTCAGTAGAAAAGGT 57.359 40.909 0.00 0.00 37.29 3.50
2221 2313 5.755409 TGGCAGATTCAGTAGAAAAGGTA 57.245 39.130 0.00 0.00 37.29 3.08
2222 2314 6.313519 TGGCAGATTCAGTAGAAAAGGTAT 57.686 37.500 0.00 0.00 37.29 2.73
2223 2315 6.115446 TGGCAGATTCAGTAGAAAAGGTATG 58.885 40.000 0.00 0.00 37.29 2.39
2224 2316 5.529060 GGCAGATTCAGTAGAAAAGGTATGG 59.471 44.000 0.00 0.00 37.29 2.74
2225 2317 5.008118 GCAGATTCAGTAGAAAAGGTATGGC 59.992 44.000 0.00 0.00 37.29 4.40
2226 2318 6.115446 CAGATTCAGTAGAAAAGGTATGGCA 58.885 40.000 0.00 0.00 37.29 4.92
2227 2319 6.599244 CAGATTCAGTAGAAAAGGTATGGCAA 59.401 38.462 0.00 0.00 37.29 4.52
2228 2320 7.121168 CAGATTCAGTAGAAAAGGTATGGCAAA 59.879 37.037 0.00 0.00 37.29 3.68
2229 2321 7.836183 AGATTCAGTAGAAAAGGTATGGCAAAT 59.164 33.333 0.00 0.00 37.29 2.32
2230 2322 7.775053 TTCAGTAGAAAAGGTATGGCAAATT 57.225 32.000 0.00 0.00 0.00 1.82
2231 2323 7.391148 TCAGTAGAAAAGGTATGGCAAATTC 57.609 36.000 0.00 0.00 0.00 2.17
2232 2324 6.945435 TCAGTAGAAAAGGTATGGCAAATTCA 59.055 34.615 0.00 0.00 0.00 2.57
2233 2325 7.121168 TCAGTAGAAAAGGTATGGCAAATTCAG 59.879 37.037 0.00 0.00 0.00 3.02
2234 2326 6.948309 AGTAGAAAAGGTATGGCAAATTCAGT 59.052 34.615 0.00 0.00 0.00 3.41
2235 2327 8.107095 AGTAGAAAAGGTATGGCAAATTCAGTA 58.893 33.333 0.00 0.00 0.00 2.74
2361 2459 8.647143 ATCTTACAAAAATGTCACCAACAAAG 57.353 30.769 0.00 0.00 42.37 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.176680 CTATGCTGCCTCACGGAACT 59.823 55.000 0.00 0.00 0.00 3.01
29 30 0.032678 CTACCCTATGCTGCCTCACG 59.967 60.000 0.00 0.00 0.00 4.35
78 79 0.595095 CTTGTGGCCTTGACTTCTGC 59.405 55.000 3.32 0.00 0.00 4.26
106 108 4.112634 GCTTGACAATATCGTACAGCTGA 58.887 43.478 23.35 0.48 0.00 4.26
169 171 3.064207 GTGTGGTCATTACGCTTTCAGA 58.936 45.455 0.00 0.00 0.00 3.27
331 338 7.094890 GCATTGTATGATCTTGGTTCTATCCAG 60.095 40.741 0.00 0.00 38.80 3.86
336 343 5.912892 TCGCATTGTATGATCTTGGTTCTA 58.087 37.500 0.00 0.00 0.00 2.10
389 396 1.228583 AGTGGCCTCACAGACTCGA 60.229 57.895 3.32 0.00 45.91 4.04
424 432 4.881273 GTCAATCCCACATGCAACTACATA 59.119 41.667 0.00 0.00 0.00 2.29
576 584 6.486320 TCACACATTTCTTCATTGTGAGCTTA 59.514 34.615 9.08 0.00 41.20 3.09
903 924 9.301153 ACAATGATTTAAAAAGATATTGTCGGC 57.699 29.630 0.00 0.00 33.46 5.54
1000 1030 2.885554 GCTCTTGGAACATGGGGAACAT 60.886 50.000 0.00 0.00 39.30 2.71
1030 1060 0.962356 CACTTGTCATGTGGGCCCTC 60.962 60.000 25.70 21.33 0.00 4.30
1060 1091 1.154225 GGTCAAGGCAAATCGCGTG 60.154 57.895 5.77 0.00 43.84 5.34
1354 1389 6.625873 AGAAAAGAATCAGGTCAACTCAAC 57.374 37.500 0.00 0.00 0.00 3.18
1454 1491 0.035317 AGCTCAACGACCATTGCAGA 59.965 50.000 0.00 0.00 0.00 4.26
1536 1574 8.378565 TCTTGACAACTTCCTCTATGAAATCTT 58.621 33.333 0.00 0.00 0.00 2.40
1540 1578 7.041098 GCTTTCTTGACAACTTCCTCTATGAAA 60.041 37.037 0.00 0.00 0.00 2.69
1554 1592 5.398603 TTTCTTGTTGGCTTTCTTGACAA 57.601 34.783 0.00 0.00 31.69 3.18
1576 1614 2.028112 AGCACCACGTGATCACTTGTAT 60.028 45.455 25.46 13.95 35.23 2.29
1779 1818 2.881441 ACGTAGTTGCTGTCACACG 58.119 52.632 0.00 0.00 37.78 4.49
1822 1863 5.990120 AACTAGTACTACCAACCACGAAT 57.010 39.130 0.00 0.00 0.00 3.34
1882 1924 7.433708 AATCGTGTTGATCAACTACATTTGA 57.566 32.000 32.57 21.24 41.67 2.69
1979 2024 0.953727 ACGGCTGTGTACGAACTACA 59.046 50.000 0.00 0.00 32.53 2.74
2007 2052 6.370994 AGTTGAAACAATCACATGCAAAAACA 59.629 30.769 0.00 0.00 37.92 2.83
2158 2204 3.009253 TGCCATGCCTTTTCCATTGAATT 59.991 39.130 0.00 0.00 0.00 2.17
2213 2305 6.071616 TGGTACTGAATTTGCCATACCTTTTC 60.072 38.462 0.00 0.00 34.42 2.29
2214 2306 5.777732 TGGTACTGAATTTGCCATACCTTTT 59.222 36.000 0.00 0.00 34.42 2.27
2215 2307 5.185056 GTGGTACTGAATTTGCCATACCTTT 59.815 40.000 0.00 0.00 34.42 3.11
2216 2308 4.705023 GTGGTACTGAATTTGCCATACCTT 59.295 41.667 0.00 0.00 34.42 3.50
2217 2309 4.263727 TGTGGTACTGAATTTGCCATACCT 60.264 41.667 0.00 0.00 34.42 3.08
2218 2310 4.013728 TGTGGTACTGAATTTGCCATACC 58.986 43.478 0.00 0.00 33.99 2.73
2219 2311 4.457603 TGTGTGGTACTGAATTTGCCATAC 59.542 41.667 5.91 5.91 40.30 2.39
2220 2312 4.457603 GTGTGTGGTACTGAATTTGCCATA 59.542 41.667 0.00 0.00 0.00 2.74
2221 2313 3.255642 GTGTGTGGTACTGAATTTGCCAT 59.744 43.478 0.00 0.00 0.00 4.40
2222 2314 2.621055 GTGTGTGGTACTGAATTTGCCA 59.379 45.455 0.00 0.00 0.00 4.92
2223 2315 2.350388 CGTGTGTGGTACTGAATTTGCC 60.350 50.000 0.00 0.00 0.00 4.52
2224 2316 2.350388 CCGTGTGTGGTACTGAATTTGC 60.350 50.000 0.00 0.00 0.00 3.68
2225 2317 2.225491 CCCGTGTGTGGTACTGAATTTG 59.775 50.000 0.00 0.00 0.00 2.32
2226 2318 2.500229 CCCGTGTGTGGTACTGAATTT 58.500 47.619 0.00 0.00 0.00 1.82
2227 2319 1.271163 CCCCGTGTGTGGTACTGAATT 60.271 52.381 0.00 0.00 0.00 2.17
2228 2320 0.323629 CCCCGTGTGTGGTACTGAAT 59.676 55.000 0.00 0.00 0.00 2.57
2229 2321 1.749665 CCCCGTGTGTGGTACTGAA 59.250 57.895 0.00 0.00 0.00 3.02
2230 2322 2.874664 GCCCCGTGTGTGGTACTGA 61.875 63.158 0.00 0.00 0.00 3.41
2231 2323 2.358247 GCCCCGTGTGTGGTACTG 60.358 66.667 0.00 0.00 0.00 2.74
2232 2324 2.445119 TTGCCCCGTGTGTGGTACT 61.445 57.895 0.00 0.00 0.00 2.73
2233 2325 2.111460 TTGCCCCGTGTGTGGTAC 59.889 61.111 0.00 0.00 0.00 3.34
2234 2326 1.120184 TAGTTGCCCCGTGTGTGGTA 61.120 55.000 0.00 0.00 0.00 3.25
2235 2327 2.445119 TAGTTGCCCCGTGTGTGGT 61.445 57.895 0.00 0.00 0.00 4.16
2361 2459 1.068748 CATTGGAGCACTGTGACTTGC 60.069 52.381 12.86 2.14 39.16 4.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.